Revealing the Full Proteoform Landscape with the Enhanced Power of Top-down Mass Spectrometry
Top-down proteomics offers a new window into the true complexity of protein species and promises to complement, rather than replace, traditional bottom-up methods. Here, we explore these developments and what the future might hold.
Proteomics, the large-scale study of proteins, depends on mass spectrometry (MS) as the key tool for analyzing protein structure, modifications, and function. Traditionally, this has involved approaches that require breaking proteins into their building blocks before analysis. Much like early DNA and RNA sequencing methods that relied on sequencing fragmented molecules and assembling the results, “bottom-up” proteomics digests proteins into peptides and then infers the protein’s sequence and any post-translational modifications (PTMs) from these fragments. While powerful and suitable for high-throughput analysis, this peptide-centric approach does not reveal important information about how modifications and sequence variations coexist on the same intact protein.